I have a Nest thermostat and a Netatmo system with 3 internal units.
I find that downstairs in winter stays warmer than upstairs, so I have the thermostat set at 72, but it upstairs can be 5-8 degrees cooler than downstairs.
Can I have the Nest run for a certain amount of time to have it warm the home, say 30 mins - 1hr and then turn off when it knows that the temperature upstairs (via the Netatmo) is at a certain temperature or within a certain range ?
I would suggest you just balance your HVAC system properly. Utilize the louvers on all of your vents to smooth out the temperature delta you are seeing across your house. It takes some time, but is absolutely possible and well worth it. Your winter setup will differ from your summer setup, and balance is tricky at seasonal switches of fall and spring, but mid summer and mid winter, it is absolutely possible.
(Jason "The Enabler" as deemed so by @Smart)
… And this is exactly why I want all of mine replaced with the smart vents!